filter genome above N50 value

Question

[shubhra.bhattacharya]

Hi everyone, I want to filter my assembly to get contigs above the N50 value only.

How can this be done.

--Thanks in advance

[WouterDeCoster]

You realize that your new filtered assembly will have a new, higher N50 value and you are just chasing a moving target until you have one contig left?

Answer 1

[Michael]

Calculate the N50 value, and extract all sequences with length >= N50 from your fasta file. The question is just, why? N50 is not a magical threshold below which contigs are not real.

[shubhra.bhattacharya]

Hi! I have two genomes (both draft) of an organism. I have to find out which genome between these two has to be used as a reference for my downstream analysis (transcriptome and SNP profile study etcc) For this genome-genome comparison I have used approaches such as synmap, LAST and mauve but I still cannot reach a conclusion. So, that is the reason I am wanting to filter them at N50 and see where it goes. Kindly suggest any other alternatives as well if possible.

--Thanks in advance

[GenoMax]

Have you tried to check if you can reconcile the two assemblies to see if you can make a better combined one?

[jean.elbers]

There is "newer" pipeline for combining the two assemblies called NucMerge that you might try (https://www.biorxiv.org/content/early/2018/11/30/483701), but I would first consider C: filter genome above N50 value

[Michael]

There are many:

• remapping completeness of DNA/RNA seq
• linkage map - linkage errors
• BUSCO
• estimate of contamination, e.g. by bacterial contigs
• repeat rate, GC content, assembly size vs. expected values
• ....

[shubhra.bhattacharya]

Thanks for your suggestions!